Nearly 40% of the Haemophilus (H.) influenzae genome is comprised of genes of unknown function, many of which have no recognizable functional orthologues in other species. Similar numbers of unidentified open reading frames (orfs) are present in other sequenced or partially sequenced genomes of infectious organisms. Comprehensive screens and selections for identifying functional classes of genes provide a crucial starting point for converting the vast body of growing sequence data into meaningful biological information that can be used for drug discovery.
One major and important class of genes consists of those bacterial genes that are essential for growth or viability of a bacterium. Because useful conventional antibiotics are known to act by interfering with the products of essential genes, it is likely that the discovery of new essential gene products will have a significant impact on efforts to develop novel antimicrobial drugs. Essential gene products have been traditionally identified through the isolation of conditional lethal mutants, or by transposon mutagenesis in the presence of a complementing wild type allele (balanced lethality). However, such approaches are laborious, as they require identification, purification, and study of individual mutant strains. These methods are also limited to species with well-developed systems for genetic manipulation and, therefore, cannot be readily applied to many of the potentially dangerous microorganisms whose genomes have recently been sequenced.
In order to facilitate the discovery of novel anti-microbial drugs, it would be desirable to have a rapid, generalized method of identifying essential growth/viability genes in pathogens. Such a method would be particularly useful for identifying essential genes in pathogens that are not genetically well-characterized. Such a method could also be used to identify essential genes in higher organisms, e.g., in animals and in plants.